Stream: genomics
Topic: chromosome-copy-number-change-type
Patrick Werner (Jun 06 2019 at 12:12):
Currently this component only has the value binding to copy number loss and copy number gain.
If we also want to transport: del, dup, amp, loh, ins should we extend our valueSet/Codesystem or use a new component?
Kevin Power (Jun 07 2019 at 20:31):
Is there a standardized list anywhere we could point at and reference? I am trying to remember our old Copy Number profile and if it had a LOINC that we could consider?
Also this is a fuzzy area to me. How is Copy Number Loss different from del? Copy Number Gain from duo?
Bret H (Sep 15 2019 at 16:14):
@Kevin Power @Patrick Werner Copy number change type as loss or gain is a boolean and implies more granular definition elsewhere (in the mind of the recipient).
E.g. Loss of Herterozygosity is more granular than deletion. Deletion also has additional implications beyond copy number loss. Having both LOH and copy number loss changes the component to offer the ability to describe with more or less granularity.
Is the community needing more than the boolean value set?
FYI: Not Directly related but might be helpful in finding LOINC codes specific to the component. LOINC codes for ISCN nomenclature - https://loinc.org/81291-7/ https://loinc.org/62356-1/
Bret H (Sep 15 2019 at 16:17):
81297-4 Structural variant panel
82155-3 Genomic structural variant copy number {#}
81299-0 Structural variant reported arrCGH [Ratio] C 0..1 {Ratio}
81300-6 Structural variant [Length] O 0..1 {#}
81301-4 Structural variant outer start and end O 0..1 {Range}
81302-2 Structural variant inner start and end O 0..1 {Range}
Bret H (Sep 15 2019 at 16:21):
PS https://loinc.org/62389-2/ looks like a very nice panel
Here is the specific cognate for the component https://loinc.org/62378-5/ has the boolean values
Dora Walter (Sep 15 2019 at 17:35):
Chromosome analysis master panel is overwhelming - so much information
Larry Babb (Sep 17 2019 at 14:26):
+1 @Dora Finkeisen on "overwhelming". Same goes for "Master HL7 genetic variant reporting panel" x2.
What we need is a standard to fix it! ;)
Kevin Power (Sep 17 2019 at 14:27):
I hear this HL7 V3 thing is really good, should we try it? :slight_smile:
Last updated: Apr 12 2022 at 19:14 UTC
